User: ariel.balter

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ariel.balter30
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Posts by ariel.balter

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Comment: C: MACS2 with multiple replicates
... Yeah I think you are probably correct based on the output I got. ...
written 9 days ago by ariel.balter30
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Comment: C: Why use the qvalue package instead of p.adjust in R stats?
... Hello--The link under the phrase "the same thread" points to "https://stat.ethz.ch/pipermail/bioconductor/attachments/20121219/00dc27b1/attachment.pl" which is a perl file. What link did you intend? Thanks! Something to add: When I went to the [original post](https://stat.ethz.ch/pipermail/biocondu ...
written 9 days ago by ariel.balter30
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Comment: C: extracting several columns from a file
... I would like to suggest editing the question title to include that you are trying to do this in R. For example: "Extracting several columns from a file using R." This will help other people looking for similar answers via search engines. As stated, the answer could be as simple as `man cut`. ...
written 10 days ago by ariel.balter30
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Crazy log-likelihood values from MACS2 `bdgdiff`.
... I'm trying out differential binding analysis with `macs2 bdgdiff`. I've called peaks and gotten very reasonable values for fold-changes, p-values, q-values, etc. For example: treat1_chip_repB.bed ``` 1 10006 10499 treat1_chip_repB_peak_1 109 . 2.80877 14.06537 10.98392 1 46683 47046 treat1_chip_ ...
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Comment: C: MACS2 with multiple replicates
... I just want to know what method macs2 is using. Calling multiple replicates with macs2 is part of the encode pipeline. ...
written 15 days ago by ariel.balter30
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MACS2 with multiple replicates
... When you use macs2 with [multiple replicates](https://github.com/taoliu/MACS/wiki/Build-Signal-Track#run-macs2-combining-replicates) is it just pooling the replicates or doing something more sophisticated? ...
macs2 chip-seq written 15 days ago by ariel.balter30 • updated 14 days ago by James Ashmore1.5k
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Comment: C: What does "pileup" mean in the context of MACS2 peak caller?
... But those are not counts under peaks (which I call coverage, such as is calculated with `bedtools coverage`). Those gaps are just small gaps (0-100 bp) in coordinates. And, the 4th column isn't coverage--it's a decimal number that measures _something_, but I don't know what and it's not documented. ...
written 20 days ago by ariel.balter30
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What does "pileup" mean in the context of MACS2 peak caller?
... I usually think of a "pileup" file as a file made from a bam/sam alignment that lists the coverage at each coordinate. This is what `samtools pileup` and `samtools mpileup` make. For instance, here is the output of `samtools pileup`: #chr coord base count 1 9998 n ...
macs2 chip-seq pileup written 21 days ago by ariel.balter30 • updated 21 days ago by Santosh Anand1.6k
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Comment: C: Benchmark - Comparison of Different NGS Mappers
... Good point @joe.cornish826. The OP used a data presentation style known to be a poor practice in order to show barely perceptible differences in data which is reported as a single number taken from a process that has a random component. They have no way of knowing if the differences are a complete f ...
written 10 weeks ago by ariel.balter30
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Answer: A: Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak callin
... In my case, I can ask the lab that did the sequencing, and they can tell me EXACTLY what the fragment size distribution is. I would try talking to them. The fragment size reported by the lab that did the PCR is undoubtedly going to be better than any software estimate. ...
written 10 weeks ago by ariel.balter30

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